12-47972666-G-T

Variant names:

• chr12-47972666-G-T
• rs2071358

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.213 in 152,122 control chromosomes in the GnomAD database, including 3,711 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.21 (3711 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.387
• Publications: 27 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.384 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.212 AC: 32285 AN: 152004 Hom.: 3692 Cov.: 31

Gnomad AFR AF: 0.219

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.295

Gnomad ASJ AF: 0.166

Gnomad EAS AF: 0.398

Gnomad SAS AF: 0.166

Gnomad FIN AF: 0.234

Gnomad MID AF: 0.0796

Gnomad NFE AF: 0.180

Gnomad OTH AF: 0.196

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.213 AC: 32344 AN: 152122 Hom.: 3711 Cov.: 31 AF XY: 0.216 AC XY: 16072 AN XY: 74362

African (AFR) AF: 0.219 AC: 9094 AN: 41490

American (AMR) AF: 0.296 AC: 4520 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.166 AC: 574 AN: 3468

East Asian (EAS) AF: 0.399 AC: 2062 AN: 5174

South Asian (SAS) AF: 0.164 AC: 789 AN: 4818

European-Finnish (FIN) AF: 0.234 AC: 2470 AN: 10562

Middle Eastern (MID) AF: 0.0753 AC: 22 AN: 292

European-Non Finnish (NFE) AF: 0.180 AC: 12223 AN: 68006

Other (OTH) AF: 0.201 AC: 424 AN: 2112

Alfa AF: 0.193 Hom.: 5935

Bravo AF: 0.221

Asia WGS AF: 0.282 AC: 981 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.085
DANN	Benign	0.36
PhyloP100		-0.39

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2071358; hg19: chr12-48366449;